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One theory doing the rounds is that the remains could belong to Rohilla chieftains from Bareily who fought against the British in 1857 and were killed by the British Army.
Another theory said the remains could be of those who died of epidemics, malaria or famine.
State Transport Minister Yashpal Arya visited the site last evening and directed Nagarjuna Construction company to stop construction work there which had been underway since 2014, an official release here said.
Terming the recovery of human skeletal remains in such large numbers as a serious matter, the minister said it will be investigated by conducting a DNA test of the recoveries.
The discovery was made by workers engaged in the construction of a new Inter-State Bus terminal in Gaulapar area of Haldwani on Tuesday setting off a debate among officials, experts and people in general about how old they could be, said Arya, who hails from Haldwani.
As locals say they have no memory of a burial ground being located near the ISBT site where construction work has been going on since 2014. Experts say they could date back over a hundred years.
However, Chief Minister Trivendra Singh Rawat said nothing could be said without a scientific analysis of the remains.